Methylene Blue should not be used for prolonged exposure, or in permanent (main, display) systems, as it can/will kill off necessary beneficial bacteria.
Methylene Blue is a potent phytotoxin that can target all sorts of bacteria and microorganisms, including beneficial ones. It is highly toxic to plants and can wipe out the bacteria in your aquarium biofilter.
Methylene Blue should not be used for prolonged exposure or in permanent (main, display) systems, as it can kill off necessary beneficial bacteria. However, it is a safe aquarium disinfectant that is also used to treat toxicity often caused by ammonia and nitrite.
The antibacterial qualities of Methylene Blue are increased with UV light, and given the amount of Methylene Blue ratio to water, it can kill beneficial bacteria. Methylene Blue is beneficial against superficial fungal infections in fish, and it can be used to prevent fungal diseases in fish eggs and fry.
It is also effective against several external protozoans, including Costia, Chilodonella, and Ichthyophthirius (Ich) . Methylene Blue is also effective for killing bacteria, viruses, and parasites, but it is not always efficacious.
A study conducted on mice showed that long-term methylene blue treatment can affect the composition of the gut microbiome and its relationship with the cognitive abilities of mice.